Structure of PDB 6bef Chain C Binding Site BS01

Receptor Information
>6bef Chain C (length=529) Species: 10254 (Vaccinia virus WR) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IKRSNVFAVDSQIPTLYMPQYISLSGVMTNDNQAIASFEIRDQYITALNH
LVLSLELPEVKGMGRFGYVPYVGYKCINHVSISSCNGVIWEIEGEELYNN
CINNTIALKHSGYSSELNDISIGLTPNDTIKEPSTVYVYIKTPFDVEDTF
SSLKLSDSKITVTVTFNPVSDIVIRDSSFDFETFNKEFVYVPELSFIGYM
VKNVQIKPSFIEKPRRVIGQINQPTATVTEVHAATSLSVYTKPYYGNTDN
KFISYPGYSQDEKDYIDAYVSRLLDDLVIVSDGPPTGYPESAEIVEVPED
GIVSIQDADVYVKIDNVPDNMSVYLHTNLLMFGTRKNSFIYNISKKFSAI
TGTYSDATKRTIFAHISHSINIIDTSIPVSLWTSQRNVYNGDNRSAESKA
KDLFINDPFIKGIDFKNKTDIISRLEVRFGNDVLYSENGPISRIYNELLT
KSNNGTRTLTFNFTPKIFFRPTTITANVSRGKDKLSVRVVYSTMDVNHPI
YYVQKQLVVVCNDLYKVSYDQGVSITKIM
Ligand information
Ligand ID3YI
InChIInChI=1S/C38H47NO13/c1-16-11-10-12-17(2)37(48)39-28-23(15-40)32(45)25-26(33(28)46)31(44)21(6)35-27(25)36(47)38(8,52-35)50-14-13-24(49-9)18(3)34(51-22(7)41)20(5)30(43)19(4)29(16)42/h10-16,18-20,24,29-30,34,42-46H,1-9H3,(H,39,48)/b11-10+,14-13+,17-12-/t16-,18+,19+,20+,24-,29-,30+,34+,38-/m0/s1
InChIKeyBBNQHOMJRFAQBN-UPZFVJMDSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c1(c4c(O)c(c3OC2(OC=CC(OC)C(C(OC(=O)C)C(C(O)C(C(O)C(C=CC=C(C(Nc1c(c(O)c4c3C2=O)C=O)=O)C)C)C)C)C)C)C)O
OpenEye OEToolkits 2.0.6Cc1c(c2c3c4c1OC(C4=O)(OC=CC(C(C(C(C(C(C(C(C=CC=C(C(=O)Nc(c2O)c(c3O)C=O)C)C)O)C)O)C)OC(=O)C)C)OC)C)O
CACTVS 3.385CO[CH]1C=CO[C]2(C)Oc3c(C)c(O)c4c(O)c(NC(=O)C(=CC=C[CH](C)[CH](O)[CH](C)[CH](O)[CH](C)[CH](OC(C)=O)[CH]1C)C)c(C=O)c(O)c4c3C2=O
OpenEye OEToolkits 2.0.6Cc1c(c2c3c4c1O[C@@](C4=O)(O/C=C/[C@@H]([C@H]([C@H]([C@@H]([C@@H]([C@@H]([C@H]([C@H](/C=C/C=C(\C(=O)Nc(c2O)c(c3O)C=O)/C)C)O)C)O)C)OC(=O)C)C)OC)C)O
CACTVS 3.385CO[C@H]1\C=C\O[C@@]2(C)Oc3c(C)c(O)c4c(O)c(NC(=O)\C(=C/C=C/[C@H](C)[C@H](O)[C@@H](C)[C@@H](O)[C@@H](C)[C@H](OC(C)=O)[C@@H]1C)C)c(C=O)c(O)c4c3C2=O
FormulaC38 H47 N O13
Name(2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-8-formyl-5,6,9,17,19-pentahydroxy-23-methoxy-2,4,12,16,18,20,22-heptam ethyl-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-21-yl acetate;
3-formyl rifamycin SV
ChEMBLCHEMBL3323549
DrugBank
ZINCZINC000169715894
PDB chain6bef Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6bef Structural basis for the inhibition of poxvirus assembly by the antibiotic rifampicin.
Resolution3.21 Å
Binding residue
(original residue number in PDB)		F168 F486
Binding residue
(residue number reindexed from 1)		F150 F468
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.98,Kd=104uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0042802 identical protein binding
Biological Process
GO:0046677 response to antibiotic
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6bef, PDBe:6bef, PDBj:6bef
PDBsum6bef
PubMed30068608
UniProtP68440|PG125_VACCW Scaffold protein OPG125 (Gene Name=OPG125)

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